// gdcmFile.cxx
-
+//-----------------------------------------------------------------------------
#include "gdcmFile.h"
#include "gdcmUtil.h"
#include "jpeg/ljpg/jpegless.h"
-/////////////////////////////////////////////////////////////////
+//-----------------------------------------------------------------------------
+// Constructor / Destructor
/**
* \ingroup gdcmFile
* \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
* one sets an a posteriori shadow dictionary (efficiency can be
* seen as a side effect).
*
- * @param filename file to be opened for parsing
+ * @param header file to be opened for reading datas
*
* @return
*/
-gdcmFile::gdcmFile(std::string & filename)
- :gdcmHeader(filename.c_str())
-{
- if (IsReadable())
- SetPixelDataSizeFromHeader();
+gdcmFile::gdcmFile(gdcmHeader *header) {
+ Header=header;
+ SelfHeader=false;
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
}
-gdcmFile::gdcmFile(const char * filename)
- :gdcmHeader(filename)
-{
- if (IsReadable())
+/**
+ * \ingroup gdcmFile
+ * \brief Constructor dedicated to writing a new DICOMV3 part10 compliant
+ * file (see SetFileName, SetDcmTag and Write)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * \Note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ * @param filename file to be opened for parsing
+ * @return
+ */
+gdcmFile::gdcmFile(std::string & filename) {
+ Header=new gdcmHeader(filename.c_str());
+ SelfHeader=true;
+
+ if (Header->IsReadable())
+ SetPixelDataSizeFromHeader();
+}
+
+gdcmFile::gdcmFile(const char * filename) {
+ Header=new gdcmHeader(filename);
+ SelfHeader=true;
+
+ if (Header->IsReadable())
SetPixelDataSizeFromHeader();
}
/**
* \ingroup gdcmFile
- * \brief calcule la longueur (in bytes) A ALLOUER pour recevoir les
- * pixels de l'image ou DES images dans le cas d'un multiframe
- *
- * ATTENTION : il ne s'agit PAS de la longueur du groupe des Pixels
- * (dans le cas d'images compressees, elle n'a pas de sens).
- *
- * @return longueur a allouer
+ * \brief canonical destructor
+ * \Note If the gdcmHeader is created by the gdcmFile, it is destroyed
+ * by the gdcmFile
*/
-void gdcmFile::SetPixelDataSizeFromHeader(void) {
- int nb;
- std::string str_nb;
- str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
- }
- lgrTotale = lgrTotaleRaw = GetXSize() * GetYSize() * GetZSize()
- * (nb/8)* GetSamplesPerPixel();
- std::string str_PhotometricInterpretation =
- gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
-
- /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
- // pb when undealt Segmented Palette Color
-
- if (HasLUT()) {
- lgrTotale*=3;
- }
+gdcmFile::~gdcmFile(void) {
+ if(SelfHeader)
+ delete Header;
+ Header=NULL;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \ingroup gdcmFile
+ * \brief
+ * @return
+ */
+gdcmHeader *gdcmFile::GetHeader(void) {
+ return(Header);
}
+/**
+ * \ingroup gdcmFile
+ * \brief computes the length (in bytes) to ALLOCATE to receive the
+ * image(s) pixels (multiframes taken into account)
+ * \warning : it is NOT the group 7FE0 length
+ * (no interest for compressed images).
+ * @return length to allocate
+ */
+void gdcmFile::SetPixelDataSizeFromHeader(void) {
// see PS 3.3-2003 : C.7.6.3.2.1
//
// MONOCHROME1
// YBR_ICT
// YBR_RCT
- // LUT's
- // ex : gdcm-US-ALOKA-16.dcm
- // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
- // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
- // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
+ // LUT's
+ // ex : gdcm-US-ALOKA-16.dcm
+ // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
+ // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
- // ex : OT-PAL-8-face.dcm
- // 0028|1201 [US] [Red Palette Color Lookup Table Data]
- // 0028|1202 [US] [Green Palette Color Lookup Table Data]
- // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+ // ex : OT-PAL-8-face.dcm
+ // 0028|1201 [US] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [US] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
-
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief Returns the size (in bytes) of required memory to hold
- * \ the pixel data represented in this file, when user DOESN'T want
- * \ to get RGB pixels image when it's stored as a PALETTE COLOR image
- * \ - the (vtk) user is supposed to know how deal with LUTs -
- * \ warning to be used with GetImagePixelsRaw()
- * @return The size of pixel data in bytes.
- */
-
-size_t gdcmFile::GetImageDataSizeRaw(void) {
- return (lgrTotaleRaw);
+ int nb;
+ std::string str_nb;
+ str_nb=Header->GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ if (nb == 12) nb =16;
+ }
+ lgrTotale = lgrTotaleRaw = Header->GetXSize() * Header->GetYSize()
+ * Header->GetZSize() * (nb/8)* Header->GetSamplesPerPixel();
+ std::string str_PhotometricInterpretation =
+ Header->GetEntryByNumber(0x0028,0x0004);
+
+ /*if ( str_PhotometricInterpretation == "PALETTE COLOR " )*/
+ // pb when undealt Segmented Palette Color
+
+ if (Header->HasLUT()) {
+ lgrTotale*=3;
+ }
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Returns the size (in bytes) of required memory to hold
* the pixel data represented in this file.
* @return The size of pixel data in bytes.
*/
-
size_t gdcmFile::GetImageDataSize(void) {
return (lgrTotale);
}
-
-/////////////////////////////////////////////////////////////////
/**
- * \ingroup gdcmFile
- * \brief Read pixel data from disk (optionaly decompressing) into the
- * caller specified memory location.
- * @param destination where the pixel data should be stored.
- *
+ * \ingroup gdcmFile
+ * \brief Returns the size (in bytes) of required memory to hold
+ * \ the pixel data represented in this file, when user DOESN'T want
+ * \ to get RGB pixels image when it's stored as a PALETTE COLOR image
+ * \ - the (vtk) user is supposed to know how deal with LUTs -
+ * \warning to be used with GetImagePixelsRaw()
+ * @return The size of pixel data in bytes.
*/
-bool gdcmFile::ReadPixelData(void* destination) {
-
- if ( !OpenFile())
- return false;
-
- if ( fseek(fp, GetPixelOffset(), SEEK_SET) == -1 ) {
- CloseFile();
- return false;
- }
-
-
- // ---------------------- Compacted File (12 Bits Per Pixel)
-
- /* unpack 12 Bits pixels into 16 Bits pixels */
- /* 2 pixels 12bit = [0xABCDEF] */
- /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */
-
- if (GetBitsAllocated()==12) {
- int nbPixels = GetXSize()*GetYSize();
- unsigned char b0, b1, b2;
-
- unsigned short int* pdestination = (unsigned short int*)destination;
- for(int p=0;p<nbPixels;p+=2) {
- fread(&b0,1,1,fp);
- fread(&b1,1,1,fp);
- fread(&b2,1,1,fp);
- //Two steps is necessary to please VC++
- *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
- /* A */ /* B */ /* D */
- *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
- /* F */ /* C */ /* E */
-
- // Troubles expected on Big-Endian processors ?
- }
- return(true);
- }
-
- // ---------------------- Uncompressed File
-
- if ( !IsDicomV3() ||
- IsImplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRLittleEndianTransferSyntax() ||
- IsExplicitVRBigEndianTransferSyntax() ||
- IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
-
- size_t ItemRead = fread(destination, GetPixelAreaLength(), 1, fp);
-
- if ( ItemRead != 1 ) {
- CloseFile();
- return false;
- } else {
- CloseFile();
- return true;
- }
- }
-
- // ---------------------- Run Length Encoding
-
- if (gdcmHeader::IsRLELossLessTransferSyntax()) {
- int res = (bool)gdcm_read_RLE_file (destination);
- return res;
- }
-
- // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
-
- int nb;
- std::string str_nb=gdcmHeader::GetPubElValByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
- }
- int nBytes= nb/8;
-
- int taille = GetXSize() * GetYSize() * GetSamplesPerPixel();
- long fragmentBegining; // for ftell, fseek
-
- bool jpg2000 = IsJPEG2000();
- bool jpgLossless = IsJPEGLossless();
-
- bool res = true;
- guint16 ItemTagGr,ItemTagEl;
- int ln;
-
- // Position on begining of Jpeg Pixels
-
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item length
-
- if (ln != 0) {
- // What is it used for ?!?
- char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
- fread(BasicOffsetTableItemValue,ln,1,fp);
- }
-
- // first Fragment initialisation
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
-
- // parsing fragments until Sequence Delim. Tag found
-
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
-
- // --- for each Fragment
-
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Fragment Item length
-
- fragmentBegining=ftell(fp);
-
- if (jpg2000) { // JPEG 2000 : call to ???
-
- res = (bool)gdcm_read_JPEG2000_file (destination); // Not Yet written
-
- } // ------------------------------------- endif (JPEG2000)
-
- else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
-
- JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
- (unsigned short *)destination,
- GetPixelSize()*8* GetSamplesPerPixel(),
- ln);
- res=1; // in order not to break the loop
-
- } // ------------------------------------- endif (JPEGLossless)
-
- else { // JPEG Lossy : call to IJG 6b
-
- if (GetBitsStored() == 8) {
- res = (bool)gdcm_read_JPEG_file (destination); // Reading Fragment pixels
- } else {
- res = (bool)gdcm_read_JPEG_file12 (destination);// Reading Fragment pixels
- }
- } // ------------------------------------- endif (JPEGLossy)
-
- if (!res) break;
-
- destination = (char *)destination + taille * nBytes; // location in user's memory
- // for next fragment (if any)
-
- fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
- fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
-
- ItemTagGr = ItemTagEl =0;
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
-
- } // endWhile parsing fragments until Sequence Delim. Tag found
-
- return res;
-}
+size_t gdcmFile::GetImageDataSizeRaw(void) {
+ return (lgrTotaleRaw);
+}
/**
* \ingroup gdcmFile
* \brief Allocates necessary memory, copies the pixel data
* (image[s]/volume[s]) to newly allocated zone.
* Transforms YBR pixels into RGB pixels if any
- Transforms 3 planes R, G, B into a single RGB Plane
- Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * Transforms 3 planes R, G, B into a single RGB Plane
+ * Transforms single Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
* \ NULL if alloc fails
*/
return(PixelData);
}
-/**
- * \ingroup gdcmFile
- * \brief Allocates necessary memory, copies the pixel data
- * (image[s]/volume[s]) to newly allocated zone.
- * Transforms YBR pixels into RGB pixels if any
- Transforms 3 planes R, G, B into a single RGB Plane
- DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
- * @return Pointer to newly allocated pixel data.
- * \ NULL if alloc fails
- */
-void * gdcmFile::GetImageDataRaw (void) {
- if (HasLUT())
- lgrTotale /= 3; // TODO Let gdcmHeadar user a chance
- // to get the right value
- // Create a member lgrTotaleRaw ???
- PixelData = (void *) malloc(lgrTotale);
- if (PixelData)
- GetImageDataIntoVectorRaw(PixelData, lgrTotale);
- return(PixelData);
-}
-
/**
* \ingroup gdcmFile
* \brief Copies at most MaxSize bytes of pixel data to caller's
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
-
size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t MaxSize) {
-
size_t l = GetImageDataIntoVectorRaw (destination, MaxSize);
- if (!HasLUT())
+ if (!Header->HasLUT())
return lgrTotale;
- // from Lut R + Lut G + Lut B
-
+ // from Lut R + Lut G + Lut B
unsigned char * newDest = (unsigned char *)malloc(lgrTotale);
unsigned char * a = (unsigned char *)destination;
- unsigned char * lutRGBA = (unsigned char *)GetLUTRGBA();
+ unsigned char * lutRGBA = Header->GetLUTRGBA();
if (lutRGBA) {
int l = lgrTotaleRaw;
memmove(newDest, destination, l);// move Gray pixels to temp area
// CreateOrReplaceIfExist ?
std::string spp = "3"; // Samples Per Pixel
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
std::string rgb= "RGB "; // Photometric Interpretation
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
std::string planConfig = "0"; // Planar Configuration
- gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006);
-
-
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
+
} else {
// need to make RGB Pixels (?)
// from grey Pixels (?!)
// and Gray Lut (!?!)
// or Segmented xxx Palette Color Lookup Table Data and so on
-
- // Well . I'll wait till I find such an image
-
- // Oops! I get one (gdcm-US-ALOKA-16.dcm)
- // No idea how to manage it
- // It seems that *no Dicom Viewer* has any idea :-(
- // Segmented xxx Palette Color are *more* than 65535 long ?!?
+
+ // Oops! I get one (gdcm-US-ALOKA-16.dcm)
+ // No idea how to manage such an image
+ // It seems that *no Dicom Viewer* has any idea :-(
+ // Segmented xxx Palette Color are *more* than 65535 long ?!?
std::string rgb= "MONOCHROME1 "; // Photometric Interpretation
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
-
- }
-
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
+ }
// TODO : Drop Palette Color out of the Header?
return lgrTotale;
}
-
+/**
+ * \ingroup gdcmFile
+ * \brief Allocates necessary memory, copies the pixel data
+ * (image[s]/volume[s]) to newly allocated zone.
+ * Transforms YBR pixels into RGB pixels if any
+ * Transforms 3 planes R, G, B into a single RGB Plane
+ * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * @return Pointer to newly allocated pixel data.
+ * \ NULL if alloc fails
+ */
+void * gdcmFile::GetImageDataRaw (void) {
+ if (Header->HasLUT())
+ lgrTotale /= 3; // TODO Let gdcmHeadar user a chance
+ // to get the right value
+ // Create a member lgrTotaleRaw ???
+ PixelData = (void *) malloc(lgrTotale);
+ if (PixelData)
+ GetImageDataIntoVectorRaw(PixelData, lgrTotale);
+ return(PixelData);
+}
/**
* \ingroup gdcmFile
* (for some axis related reasons?). Hence he will have
* to load the image line by line, starting from the end.
* VTK users hace to call GetImageData
- * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
+ * \warning DOES NOT transform the Grey Plane + Palette Color (if any)
* into a single RGB Pixels Plane
* the (VTK) user will manage the palettes
*
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
-
size_t gdcmFile::GetImageDataIntoVectorRaw (void* destination, size_t MaxSize) {
int nb, nbu, highBit, signe;
(void)ReadPixelData(destination);
- // Nombre de Bits Alloues pour le stockage d'un Pixel
- str_nb = GetPubElValByNumber(0x0028,0x0100);
+ // Number of Bits Allocated for storing a Pixel
+ str_nb = Header->GetEntryByNumber(0x0028,0x0100);
if (str_nb == GDCM_UNFOUND ) {
nb = 16;
} else {
nb = atoi(str_nb.c_str() );
- }
-
- // Nombre de Bits Utilises
- str_nbu=GetPubElValByNumber(0x0028,0x0101);
+ }
+ // Number of Bits actually used
+ str_nbu=Header->GetEntryByNumber(0x0028,0x0101);
if (str_nbu == GDCM_UNFOUND ) {
nbu = nb;
} else {
nbu = atoi(str_nbu.c_str() );
- }
-
- // Position du Bit de Poids Fort
- str_highBit=GetPubElValByNumber(0x0028,0x0102);
+ }
+ // High Bit Position
+ str_highBit=Header->GetEntryByNumber(0x0028,0x0102);
if (str_highBit == GDCM_UNFOUND ) {
highBit = nb - 1;
} else {
// Pixel sign
// 0 = Unsigned
// 1 = Signed
- str_signe=GetPubElValByNumber(0x0028,0x0103);
+ str_signe=Header->GetEntryByNumber(0x0028,0x0103);
if (str_signe == GDCM_UNFOUND ) {
signe = 0; // default is unsigned
} else {
signe = atoi(str_signe.c_str() );
}
- // re arange bytes inside the integer
+ // re arange bytes inside the integer (processor endianity)
if (nb != 8)
- SwapZone(destination, GetSwapCode(), lgrTotale, nb);
+ SwapZone(destination, Header->GetSwapCode(), lgrTotale, nb);
// to avoid pb with some xmedcon breakers images
if (nb==16 && nbu<nb && signe==0) {
return (size_t)0;
}
}
-
+// DO NOT remove this code commented out.
+// Nobody knows what's expecting you ...
// Just to 'see' what was actually read on disk :-(
-// Some troubles expected
// FILE * f2;
// f2 = fopen("SpuriousFile.raw","wb");
// fwrite(destination,lgrTotale,1,f2);
// -------------------
std::string str_PhotometricInterpretation =
- gdcmHeader::GetPubElValByNumber(0x0028,0x0004);
+ Header->GetEntryByNumber(0x0028,0x0004);
if ( (str_PhotometricInterpretation == "MONOCHROME1 ")
|| (str_PhotometricInterpretation == "MONOCHROME2 ") ) {
// PhotometricInterpretation=PALETTE COLOR
// and heuristic has to be found :-(
- int planConf=GetPlanarConfiguration(); // 0028,0006
+ int planConf=Header->GetPlanarConfiguration(); // 0028,0006
// Whatever Planar Configuration is,
// "PALETTE COLOR " implies that we deal with the palette.
{
if (str_PhotometricInterpretation == "YBR_FULL") {
- // Warning : YBR_FULL_422 acts as RGB
- // : we need to make RGB Pixels from Planes Y,cB,cR
- // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
- // for code optimisation
+ // Warning : YBR_FULL_422 acts as RGB
+ // : we need to make RGB Pixels from Planes Y,cB,cR
// to see the tricks about YBR_FULL, YBR_FULL_422,
// YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
// ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
// and be *very* affraid
//
- int l = GetXSize()*GetYSize();
- int nbFrames = GetZSize();
+ int l = Header->GetXSize()*Header->GetYSize();
+ int nbFrames = Header->GetZSize();
unsigned char * newDest = (unsigned char*) malloc(lgrTotale);
unsigned char *x = newDest;
unsigned char * a = (unsigned char *)destination;
unsigned char * b = a + l;
unsigned char * c = b + l;
-
double R,G,B;
// TODO : Replace by the 'well known'
// integer computation counterpart
+ // see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf
+ // for code optimisation
+
for (int i=0;i<nbFrames;i++) {
for (int j=0;j<l; j++) {
R= 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5;
} else {
// need to make RGB Pixels from R,G,B Planes
- // (all the Frames at a time)
+ // (all the Frames at a time)
- int l = GetXSize()*GetYSize()*GetZSize();
+ int l = Header->GetXSize()*Header->GetYSize()*Header->GetZSize();
char * newDest = (char*) malloc(lgrTotale);
char * x = newDest;
*(x++) = *(a++);
*(x++) = *(b++);
*(x++) = *(c++);
- }
-
+ }
memmove(destination,newDest,lgrTotale);
free(newDest);
- }
-
+ }
break;
- }
-
+ }
case 2:
// Palettes were found
- // Let the user deal with them !
- return lgrTotale;
+ // Let the user deal with them !
+ return lgrTotale;
}
- // now, it's an RGB image
- // Lets's write it in the Header
-
- // CreateOrReplaceIfExist ?
-
+ // now, it's an RGB image
+ // Lets's write it in the Header
+ // CreateOrReplaceIfExist ?
std::string spp = "3"; // Samples Per Pixel
- gdcmHeader::SetPubElValByNumber(spp,0x0028,0x0002);
+ Header->SetEntryByNumber(spp,0x0028,0x0002);
std::string rgb="RGB "; // Photometric Interpretation
- gdcmHeader::SetPubElValByNumber(rgb,0x0028,0x0004);
+ Header->SetEntryByNumber(rgb,0x0028,0x0004);
std::string planConfig = "0"; // Planar Configuration
- gdcmHeader::SetPubElValByNumber(planConfig,0x0028,0x0006);
+ Header->SetEntryByNumber(planConfig,0x0028,0x0006);
// TODO : Drop Palette Color out of the Header?
-
return lgrTotale;
}
-
-
-/**
- * \ingroup gdcmFile
- * \brief Swap the bytes, according to swap code.
- * \warning not end user intended
- * @param im area to deal with
- * @param swap swap code
- * @param lgr Area Length
- * @param nb Pixels Bit number
- */
-
-void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
-guint32 s32;
-guint16 fort,faible;
-int i;
-
-if(nb == 16)
- switch(swap) {
- case 0:
- case 12:
- case 1234:
- break;
-
- case 21:
- case 3412:
- case 2143:
- case 4321:
-
- for(i=0;i<lgr;i++)
- ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
- | ((((unsigned short int*)im)[i])<<8);
- break;
-
- default:
- printf("valeur de SWAP (16 bits) not allowed : %d\n", swap);
- }
-
-if( nb == 32 )
- switch (swap) {
- case 0:
- case 1234:
- break;
-
- case 4321:
- for(i=0;i<lgr;i++) {
- faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 4321 */
- fort =((unsigned long int*)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=faible;
- ((unsigned long int*)im)[i]=(s32<<16)|fort;
- }
- break;
-
- case 2143:
- for(i=0;i<lgr;i++) {
- faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 2143 */
- fort=((unsigned long int*)im)[i]>>16;
- fort= (fort>>8) | (fort<<8);
- faible=(faible>>8) | (faible<<8);
- s32=fort;
- ((unsigned long int*)im)[i]=(s32<<16)|faible;
- }
- break;
-
- case 3412:
- for(i=0;i<lgr;i++) {
- faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 3412 */
- fort=((unsigned long int*)im)[i]>>16;
- s32=faible;
- ((unsigned long int*)im)[i]=(s32<<16)|fort;
- }
- break;
-
- default:
- printf(" SWAP value (32 bits) not allowed : %d\n", swap);
- }
-return;
-}
-
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief TODO JPR
* @param inData
* @param ExpectedSize
*
- * @return integer acts as a boolean
+ * @return boolean
*/
-int gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
- SetImageDataSize(ExpectedSize);
+bool gdcmFile::SetImageData(void * inData, size_t ExpectedSize) {
+ Header->SetImageDataSize(ExpectedSize);
PixelData = inData;
lgrTotale = ExpectedSize;
- return(1);
-}
-
-
-/////////////////////////////////////////////////////////////////
-/**
- * \ingroup gdcmFile
- * \brief Sets the Pixel Area size in the Header
- * --> not-for-rats function
- *
- * \warning WARNING doit-etre etre publique ?
- * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions
- *
- * @param ImageDataSize new Pixel Area Size
- * warning : nothing else is checked
- */
-
-void gdcmFile::SetImageDataSize(size_t ImageDataSize) {
- std::string content1;
- char car[20];
- // Assumes ElValue (0x7fe0, 0x0010) exists ...
- sprintf(car,"%d",ImageDataSize);
-
- gdcmElValue*a = GetElValueByNumber(0x7fe0, 0x0010);
- a->SetLength(ImageDataSize);
-
- ImageDataSize+=8;
- sprintf(car,"%d",ImageDataSize);
- content1=car;
- SetPubElValByNumber(content1, 0x7fe0, 0x0000);
+ return(true);
}
-
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Ecrit sur disque les pixels d'UNE image
* Ca sera à l'utilisateur d'appeler son Reader correctement
* (Equivalent a IdImaWriteRawFile)
*
- * @param fileName
- * @return
+ * @param fileName name of the file to be created
+ * (any already existing file is over written)
+ * @return false if write fails
*/
-int gdcmFile::WriteRawData (std::string fileName) {
+bool gdcmFile::WriteRawData (std::string fileName) {
FILE * fp1;
fp1 = fopen(fileName.c_str(),"wb");
if (fp1 == NULL) {
printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
- return (0);
+ return (false);
}
fwrite (PixelData,lgrTotale, 1, fp1);
fclose (fp1);
- return(1);
+ return(true);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Ecrit sur disque UNE image Dicom
* Ca fonctionnera correctement (?) sur processeur Intel
* (Equivalent a IdDcmWrite)
*
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmImplVR (std::string fileName) {
+bool gdcmFile::WriteDcmImplVR (std::string fileName) {
return WriteBase(fileName, ImplicitVR);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmImplVR (const char* fileName) {
+bool gdcmFile::WriteDcmImplVR (const char* fileName) {
return WriteDcmImplVR (std::string (fileName));
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteDcmExplVR (std::string fileName) {
+bool gdcmFile::WriteDcmExplVR (std::string fileName) {
return WriteBase(fileName, ExplicitVR);
}
-/////////////////////////////////////////////////////////////////
/**
* \ingroup gdcmFile
* \brief Ecrit au format ACR-NEMA sur disque l'entete et les pixels
* (a l'attention des logiciels cliniques
* qui ne prennent en entrée QUE des images ACR ...
- * \warning si un header DICOM est fourni en entree,
- * les groupes < 0x0008 et les groupes impairs sont ignores)
- * \warning Aucun test n'est fait sur l'"Endiannerie" du processeur.
+ * \warning if a DICOM_V3 header is supplied,
+ * groups < 0x0008 and shadow groups are ignored)
+ * \warning NO TEST is performed on processor "Endiannity".
* Ca fonctionnera correctement (?) sur processeur Intel
* (Equivalent a IdDcmWrite)
*
- * @param fileName
- * @return int acts as a boolean
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
*/
-int gdcmFile::WriteAcr (std::string fileName) {
+bool gdcmFile::WriteAcr (std::string fileName) {
return WriteBase(fileName, ACR);
}
-/////////////////////////////////////////////////////////////////
+//-----------------------------------------------------------------------------
+// Protected
/**
* \ingroup gdcmFile
*
- * @param FileName
- * @param type
- *
- * @return int acts as a boolean
+* @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @param type file type (ExplicitVR, ImplicitVR, ...)
+ * @return false if write fails
*/
-int gdcmFile::WriteBase (std::string FileName, FileType type) {
+bool gdcmFile::WriteBase (std::string fileName, FileType type) {
FILE * fp1;
- fp1 = fopen(FileName.c_str(),"wb");
+ fp1 = fopen(fileName.c_str(),"wb");
if (fp1 == NULL) {
- printf("Echec ouverture (ecriture) Fichier [%s] \n",FileName.c_str());
- return (0);
+ printf("Echec ouverture (ecriture) Fichier [%s] \n",fileName.c_str());
+ return (false);
}
if ( (type == ImplicitVR) || (type == ExplicitVR) ) {
// just before writting ...
std::string rows, columns;
- if ( filetype == ACR_LIBIDO){
- rows = GetPubElValByNumber(0x0028, 0x0010);
- columns = GetPubElValByNumber(0x0028, 0x0011);
- SetPubElValByNumber(columns, 0x0028, 0x0010);
- SetPubElValByNumber(rows , 0x0028, 0x0011);
+ if ( Header->GetFileType() == ACR_LIBIDO){
+ rows = Header->GetEntryByNumber(0x0028, 0x0010);
+ columns = Header->GetEntryByNumber(0x0028, 0x0011);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0010);
+ Header->SetEntryByNumber(rows , 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
- gdcmHeader::Write(fp1, type);
+ Header->Write(fp1, type);
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
// ...and we restore the Header to be Dicom Compliant again
// just after writting
- if (filetype == ACR_LIBIDO){
- SetPubElValByNumber(rows , 0x0028, 0x0010);
- SetPubElValByNumber(columns, 0x0028, 0x0011);
+ if (Header->GetFileType() == ACR_LIBIDO){
+ Header->SetEntryByNumber(rows , 0x0028, 0x0010);
+ Header->SetEntryByNumber(columns, 0x0028, 0x0011);
}
// ----------------- End of Special Patch ----------------
fwrite(PixelData, lgrTotale, 1, fp1);
fclose (fp1);
- return(1);
+ return(true);
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/**
+ * \ingroup gdcmFile
+ * \brief Swap the bytes, according to swap code.
+ * \warning not end user intended
+ * @param im area to deal with
+ * @param swap swap code
+ * @param lgr Area Length
+ * @param nb Pixels Bit number
+ */
+void gdcmFile::SwapZone(void* im, int swap, int lgr, int nb) {
+guint32 s32;
+guint16 fort,faible;
+int i;
+
+if(nb == 16)
+ switch(swap) {
+ case 0:
+ case 12:
+ case 1234:
+ break;
+
+ case 21:
+ case 3412:
+ case 2143:
+ case 4321:
+
+ for(i=0;i<lgr;i++)
+ ((unsigned short int*)im)[i]= ((((unsigned short int*)im)[i])>>8)
+ | ((((unsigned short int*)im)[i])<<8);
+ break;
+
+ default:
+ printf("SWAP value (16 bits) not allowed : %d\n", swap);
+ }
+
+if( nb == 32 )
+ switch (swap) {
+ case 0:
+ case 1234:
+ break;
+
+ case 4321:
+ for(i=0;i<lgr;i++) {
+ faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 4321 */
+ fort =((unsigned long int*)im)[i]>>16;
+ fort= (fort>>8) | (fort<<8);
+ faible=(faible>>8) | (faible<<8);
+ s32=faible;
+ ((unsigned long int*)im)[i]=(s32<<16)|fort;
+ }
+ break;
+
+ case 2143:
+ for(i=0;i<lgr;i++) {
+ faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 2143 */
+ fort=((unsigned long int*)im)[i]>>16;
+ fort= (fort>>8) | (fort<<8);
+ faible=(faible>>8) | (faible<<8);
+ s32=fort;
+ ((unsigned long int*)im)[i]=(s32<<16)|faible;
+ }
+ break;
+
+ case 3412:
+ for(i=0;i<lgr;i++) {
+ faible= ((unsigned long int*)im)[i]&0x0000ffff; /* 3412 */
+ fort=((unsigned long int*)im)[i]>>16;
+ s32=faible;
+ ((unsigned long int*)im)[i]=(s32<<16)|fort;
+ }
+ break;
+
+ default:
+ printf("SWAP value (32 bits) not allowed : %d\n", swap);
+ }
+return;
+}
+
+/**
+ * \ingroup gdcmFile
+ * \brief Read pixel data from disk (optionaly decompressing) into the
+ * caller specified memory location.
+ * @param destination where the pixel data should be stored.
+ *
+ */
+bool gdcmFile::ReadPixelData(void* destination) {
+
+ FILE *fp;
+
+ if ( !(fp=Header->OpenFile()))
+ return false;
+
+ if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) {
+ Header->CloseFile();
+ return false;
+ }
+
+
+ // ---------------------- Compacted File (12 Bits Per Pixel)
+ /* unpack 12 Bits pixels into 16 Bits pixels */
+ /* 2 pixels 12bit = [0xABCDEF] */
+ /* 2 pixels 16bit = [0x0ABD] + [0x0FCE] */
+ if (Header->GetBitsAllocated()==12) {
+ int nbPixels = Header->GetXSize() * Header->GetYSize();
+ unsigned char b0, b1, b2;
+
+ unsigned short int* pdestination = (unsigned short int*)destination;
+ for(int p=0;p<nbPixels;p+=2) {
+ fread(&b0,1,1,fp);
+ fread(&b1,1,1,fp);
+ fread(&b2,1,1,fp);
+ //Two steps is necessary to please VC++
+ *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f);
+ /* A */ /* B */ /* D */
+ *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4);
+ /* F */ /* C */ /* E */
+
+ // Troubles expected on Big-Endian processors ?
+ }
+ return(true);
+ }
+
+ // ---------------------- Uncompressed File
+ if ( !Header->IsDicomV3() ||
+ Header->IsImplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRLittleEndianTransferSyntax() ||
+ Header->IsExplicitVRBigEndianTransferSyntax() ||
+ Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) {
+
+ size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp);
+
+ if ( ItemRead != 1 ) {
+ Header->CloseFile();
+ return false;
+ } else {
+ Header->CloseFile();
+ return true;
+ }
+ }
+
+ // ---------------------- Run Length Encoding
+ if (Header->IsRLELossLessTransferSyntax()) {
+ bool res = (bool)gdcm_read_RLE_file (fp,destination);
+ return res;
+ }
+
+ // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000
+ int nb;
+ std::string str_nb=Header->GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ if (nb == 12) nb =16; // ?? 12 should be ACR-NEMA only ?
+ }
+
+ int nBytes= nb/8;
+
+ int taille = Header->GetXSize() * Header->GetYSize()
+ * Header->GetSamplesPerPixel();
+ long fragmentBegining; // for ftell, fseek
+
+ bool jpg2000 = Header->IsJPEG2000();
+ bool jpgLossless = Header->IsJPEGLossless();
+
+ bool res = true;
+ guint16 ItemTagGr,ItemTagEl;
+ int ln;
+
+ // Position on begining of Jpeg Pixels
+
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+ fread(&ln,4,1,fp);
+ if(Header->GetSwapCode())
+ ln=Header->SwapLong(ln); // Basic Offset Table Item length
+
+ if (ln != 0) {
+ // What is it used for ?!?
+ char *BasicOffsetTableItemValue = (char *)malloc(ln+1);
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ }
+
+ // first Fragment initialisation
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+
+ // parsing fragments until Sequence Delim. Tag found
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ // --- for each Fragment
+
+ fread(&ln,4,1,fp);
+ if(Header->GetSwapCode())
+ ln=Header->SwapLong(ln); // Fragment Item length
+
+ fragmentBegining=ftell(fp);
+
+ if (jpg2000) { // JPEG 2000 : call to ???
+
+ res = (bool)gdcm_read_JPEG2000_file (fp,destination); // Not Yet written
+
+ } // ------------------------------------- endif (JPEG2000)
+
+ else if (jpgLossless) { // JPEG LossLess : call to xmedcom JPEG
+
+ JPEGLosslessDecodeImage (fp, // Reading Fragment pixels
+ (unsigned short *)destination,
+ Header->GetPixelSize()*8* Header->GetSamplesPerPixel(),
+ ln);
+ res=1; // in order not to break the loop
+
+ } // ------------------------------------- endif (JPEGLossless)
+
+ else { // JPEG Lossy : call to IJG 6b
+
+ if (Header->GetBitsStored() == 8) {
+ res = (bool)gdcm_read_JPEG_file (fp,destination); // Reading Fragment pixels
+ } else {
+ res = (bool)gdcm_read_JPEG_file12 (fp,destination);// Reading Fragment pixels
+ }
+ } // ------------------------------------- endif (JPEGLossy)
+
+ if (!res) break;
+
+ destination = (char *)destination + taille * nBytes; // location in user's memory
+ // for next fragment (if any)
+
+ fseek(fp,fragmentBegining,SEEK_SET); // To be sure we start
+ fseek(fp,ln,SEEK_CUR); // at the begining of next fragment
+
+ ItemTagGr = ItemTagEl =0;
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(Header->GetSwapCode()) {
+ ItemTagGr=Header->SwapShort(ItemTagGr);
+ ItemTagEl=Header->SwapShort(ItemTagEl);
+ }
+
+ } // endWhile parsing fragments until Sequence Delim. Tag found
+
+ Header->CloseFile();
+ return res;
}
+//-----------------------------------------------------------------------------